Op-Ed By Dr Humphrey Karamagi, WHO Representative for South Sudan

South Sudan is combating its largest and longest cholera outbreak since independence in 2011. The outbreak, which began in September 2024 has been sustained for now one year, testing the country’s experiences, defining new frontiers to interrupt transmission and providing new lessons for future similar outbreaks.

After 12 months of sustained Cholera transmission, the outbreak is slowing but has caused nearly 100 000 suspected cases and slightly over 1 500 deaths across 55 counties in 9 States and 3 Administrative Areas. The country’s multi-sectoral response—featuring surveillance, deployment of rapid response teams, medical supply prepositioning, case management, Infection Prevention and Control, Water/Sanitation/Hygiene promotion, reactive vaccination campaigns using oral cholera vaccines, and response coordination—has helped mitigate the risks to communities and saved hundreds of lives. The weekly number of new Cholera cases has drastically reduced from an average of 1000 cases at the peak of the outbreak in December 2024 to a record lowest of 114 in the last week of September 2025. The number of infected Counties declined from 55 to 7 in the same reporting period. And there was no newly infected county since June 2025.

South Sudan’s Cholera response Journey

South Sudan’s cholera outbreak was confirmed on 27 September 2024. A national Cholera outbreak was declared on 28 October. The response efforts to this day have focused on a) coordination of response actors using the Incident Management System; b) Strengthening surveillance for acute watery diarrhea (AWD), c) Laboratory diagnostics support for aetiological agents of AWD, d) Case management of acute watery diarrhea, especially severe dehydration, e) Risk communication and community engagement, f) Infection Prevention and Control, g) Water/Sanitation/Hygiene promotion, h) vaccination using Oral Cholera Vaccines, and i) Logistics.

Notably, the cholera outbreak spread so fast, reaching slightly over 27 000 cases and 472 deaths in 40 counties within the first 4 months of confirmation. The increased hostilities in Sudan, where the outbreak originated, facilitated the multiple importations into several areas of South Sudan. But even most importantly, the outbreak affected high-density areas hosting returnees/refugees’ settlements. The cholera outbreak was therefore an emergency complicating another.

Although slightly over 67 000 additional cholera cases were reported in the last 8 months, the geographical spread has been much slower with only 15 new counties reporting cases. At this one-year milestone, we should celebrate:

1. The fact that only seven of the 55 affected counties are still reporting cases, which implies that we have interrupted transmission in 48 counties

2.  More than 90 000 people successfully treated and discharged from the multiple case management centres that were set up.

3. The health workers (doctors, clinical officers, nurses, and all support staff) that continue to man our cholera treatment centres/units across the country

4. The Public Health Laboratory network that tested over 32 000 samples and confirmed 12 643 as cholera using both Rapid Diagnostic Tests and Bacterial culture. The laboratory testing of selected cases continues to provide valuable information on causative agents of the outbreak and the antibiotics sensitivity patterns that guided the treatment choices.

5. The targeted responses mounted in the flooding season, when the outbreak was projected to spiral out of control, was successful in averting the increases in cases and deaths.

6. The commitment of the partners and donors that provided the resources, including human resources from the standby partners and funding from multiple donors that we continue to use in responding to this scourge.

Over the one-year response period, the country has documented the following best practices to promote in seeking the goal of interrupting Cholera transmission:

1. Active surveillance and rigorous testing of suspected AWD cases using the Cholera RDTs as a screening tool provides Rapid detection and timely response in newly infected geographies

2.  Introduction of automated analytic products for evidence-based decision making by the national steering committee

3. Deployment of Rapid Response Teams to the newly infected counties to support verification, risk assessment and support to setting up response operations.

4.  Prioritization of Oral Rehydration Points in all infected communities as a strategy to ameliorate community mortality that was driving the case-fatality ratios higher than expected.

5.  Integration of water-quality surveillance to inform targeted communications, community engagement and promotion of safe water for domestic consumption

6. Targeted deployment of Oral Cholera vaccines to sub-county levels, instead of county-wide responses, as a strategy to shorten the turnaround times between ICG request to vaccination response dates.

WHO’s Contribution: Working Hand in Hand

Out of the WHO mandate of setting norms, standards and guidelines, the country office in South Sudan has devolved to delivery of cholera response services. We have stood alongside the Ministry of Health, communities, and partners in strengthening the foundations of care. Specifically, WHO:

1. Provided technical support to development of the multi-sectoral Cholera Prevention and Control Plan 2023-2027, which was used as the blueprint for readiness and response operations

2. Facilitated the activation of the national Public Health Emergency Operations Centre (PHEOC) that operationalized the National Incident Management system (in readiness and response operations) for effective coordination

3. Strengthened early warning and detection of acute watery diarrhea using the integrated diseases surveillance and response network. A total of 534 health facilities provided daily reporting on suspected cholera cases

4.  Provided all laboratory diagnostics tools and reagents needed used throughout the year to safely collect, transport, test and provide results to case management units as well as public health workers for evidence-based response planning and management of the outbreak.

5.  Trained 336 staff to support the different outbreak response management pillars

6. Deployed surge health workers and mobile medical teams (47 nationally coordinated RRTs to 52 counties) which needed additional pair of hands for managing the high caseloads of patients of Cholera, in order to protect continuity of essential health services.

7. WHO supported the Ministry of Health and partners to setup 102 oral rehydration points (ORPs), 88 cholera treatment units (CTUs) and 19 cholera treatment centers (CTCs) across the country to manage cases on standardized protocols and tools Facilitated awareness raising through radio talk shows, door-to-door visits, and distribution of Information, Education, and Communication (IEC) materials, including posters, flyers, and radio jingles in affected counties particularly focusing on community prevention measures for cholera.

8. Completed 17 Oral Cholera Vaccination requests to vaccinate in 55 counties, of which approvals were obtained for 48 counties (worth 10 million OCV doses). In turn, OCV deployment has been completed in 46 counties (with 2 on hold due to security related constraints) reaching 8,628,298 (84.7% of the targeted population).

9. Provided short-term (3 months) predictive analytics for Cholera outbreak trajectory to inform response planning and pre-positioning of surveillance and case management supplies

10.  In order to attain resilience and sustainable Cholera Control, WHO is facilitating the identification of Priority Areas for Multi-sectoral Interventions (PAMIs). Technical guidance, training and provision of operations support to the entire process will be guided by the WCO, with assistance from the African Regional Office Emergencies Program.

In the tail end of the Cholera outbreak, WHO re-commits to a) care and treatment of more than 71 people that are currently admitted in multiple cholera treatment centres/units in 7 counties; b) Provide care and treatment products for an additional 10,000 cases predicted for the 3-4 months ending December 2025; c) Engage the communities on context appropriate technologies for mitigating the risk of cholera infections; d) Providing education and communication materials needed to create a behavioral practices needed to interrupt Cholera transmission and e) Mobilise the resources (human, financial and materials) needed to see the end of the cholera outbreak.

At the very heart of the successful response is multisectoral collaboration led by the government. However, WHO will remain the technical and coordination agency (using the Health cluster mechanism) to support donors and response partners for the best in-class tools and technologies for Cholera control. As we head to the tail end of the outbreak, more efforts, resources and context learning will be needed. In turn, we call on the government of South Sudan, all Donors and health partners to double efforts, even when the numbers look positive.

Lesson learnt

This cholera response serves as a foundation to enhance future emergency preparedness and health system strengthening in South Sudan. Key lessons learnt include:

1. Multi-hazard preparedness plans guided pre-positioning of supplies and improved effectiveness of the outbreak response in newly affected geographies. When linked with the hazard specific preparedness and response plans, the two processes can be synergistic for effective response. The newly engaged process of identifying the Priority Areas for Multi-sectoral Interventions (PAMIs), should be used to improve the multi-year plan for sustainable Cholera control

2. Following confirmation of the Cholera outbreak on 28th September, South Sudan activated the PHEOC to active response mode in which daily meetings for coordination of the Cholera response operations were held for the first 4 months, before they were reduced to twice a week for another 2 months. The PHEOC led IMST now meets weekly and integrates management of three public health events (Cholera, Mpox, and Hepatitis E). the Activation of the Public Health Emergency Operations Center (PHEOC) at alert mode improved country readiness, laboratory diagnostics capacity, retraining of RRTs and case-management workers and pre-positioning of emergency stockpiles for responding to cholera, set up cross-border coordination, established government-led, early multi-sectoral coordination of Cholera outbreak responses. This is in addition to activation of the active surveillance and health information management drivers to inform evidence-based response interventions.

3. An incident management plan was developed and used for 6 months before it was transitioned into an annual Incident action plan. It is this incident action plan that defined the essential activities and priorities over the life of the outbreak.

4. Tailored strategies based on social and epidemiological data enhanced targeted action in Cholera outbreak response. On a routine basis, the epidemiological data were interrogated to generate inferences for targeted actions.

5. Engagement of religious and traditional leaders was one intervention that effectively strengthened community trust and compliance to the control measures considered to have influenced uptake of OCV and in turn early interruption of Cholera transmission.

6. Oral Cholera Vaccination remains a critical tool to interruption of cholera outbreaks.

7. Cross-border vaccination initiatives and regional solidarity mechanisms (EAC, IGAD, WHO) proved vital for control of cholera outbreak importations and therefore should be recommended for outbreaks in border geographies.

8. Intra-action Review (IAR) conducted 6 months into the cholera outbreak response is a good practice to promote. This not only serves IHR (2005) compliance but also feeds into improvement planning for the outbreak response operations.

9.  Lastly, an extra-ordinary inter-ministerial meeting on cholera convened by the Ministry of Health, co-chaired by the Minister of Humanitarian Affairs and Disaster Management, Hon. Albino Akol Atak, and the United Nations Deputy Special Representative of the Secretary-General, Resident and Humanitarian Coordinator (DSRSG/RC/HC) of South Sudan, Ms. Anita Kiki Gbeho. The meeting brought together several one-health line-Ministries. While this forum serves the Cholera outbreak response, it should be morphed into a unified platform to protect lives, preserve critical systems, and build national resilience to future public health and climate-related emergencies.

Call for Action

As we South Sudan moves towards the end of the current Cholera outbreak, WHO calls for a renewed collective commitment to:

1. Improve emergency preparedness by a) Conducting simulations and drills; b) Monitor implementation status of all hazards specific preparedness/response plans and c) establish a repository of tools, reports and lessons learnt for each and every Cholera outbreak.

2. Strengthen national capacity by re-training, deployment, and retention of critical health workers with skills of managing Cholera outbreak response operations.

3. Introduce molecular laboratory methods for testing and confirmation of Cholera in hard to reach or isolated geographies

4. Expand community-based systems that bring health closer to the people.

5. Secure sustainable financing to build a health system that has capacity to deal with surge in caseloads that come with outbreaks.

6. Preposition lifesaving supplies as well as deploying of medical, WASH, and nutrition supplies in high-risk counties ahead of peak flooding.

7. Introduce preventive OCV deployment for high-priority geographies defined by the PAMIs